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In the paper and implementation you add noise to the genetic component of the phenotype to reach a desired heritability using:
> g' = h * g + sqrt(1-h^2) N(0, 1), where h = heritability
There ma…
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I have recently been running a MegaPRS on some meta-analysis summary statistics and using 1000G as a reference panel. This is something I have run earlier this year (prior to version 6) and it worked …
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Take it from matteo's work. You need to fit a model between a trait from the parent(s) and a trait from the offspring. The number of parents and the trait should be a param.
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Dear Team,
I calculated partition heritability for ATAC seq peaks by using 106 GWAS sumstats.
For example: for "PASS.Schizophrenia.Trubetskoy2022 GWAS sumstats", I have 98 categories for peaks. I …
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Hello, I would like to study the genetic correlations of several diseases in East Asians, and below is the log file. I am wondering why so many SNPs are being excluded due to valid alleles QC. Could y…
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Hi,
Thank you for developing such an useful tool!
I am wondering how to obtain the estimated heritability of a disease from the return of the function ```glmmkin```. I tried the command as follows…
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Dear curators,
I was wondering if you could add an option to estimate and statistically test the heritability, more or less like GEMMA does with "PVE" in Linear Mixed Models with the kinship matrix o…
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Hello - would anyone please suggest an ANGSD way to estimate SNP-based heritability of a trait?
cheers
Misha
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Dear LCV users,
when using LCV as shown in the tutorial:
LCV = RunLCV(data[,"L2"],data[,"Z.x"],data[,"Z.y"] )
I would often get the error "NaNs produced, probably due to negative heritability est…
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Dear all,
I installed everything. I run the test files. Everything is working.
I created the summary stats based on my summary statistics.
python munge_sumstats.py --sumstats AD_META_GENOTYP…